0. emacs -Q
1. Type `M-x' and then TAB to pop up the *Completions* buffer, then type
   `C-g'.
2. Type `M-x ibuffer'.
3. Type `d' on the lines for the buffers *scratch* and *Completions* to
   flag them for deletion.
4. Type `C-c C-a' to enable ibuffer-auto-mode.
5. Type `x' and at the prompt "Really kill 2 buffers? (y or n)" type `y'.
=> The *Ibuffer* lines for  *scratch* and *Completions* are deleted and
   the echo area displays this message: "Operation finished; killed 3
   buffers".

If you change this recipe by omitting step 4, then after the buffer
lines are deleted the message displayed is "Operation finished; killed 2
buffers".

The unexpected message with ibuffer-auto-mode enabled is displayed in
Emacs 27-30 but not in Emacs 26.  With Emacs 27+, on typing `x' at step
5, the buffer *Ibuffer confirmation* pops up and a line for this buffer
immediately appears in the *Ibuffer* display, and this is counted by the
function `ibuffer-map-lines', and on typing `y' not only are the two
flagged buffers deleted, but also *Ibuffer confirmation*, hence "killed
3 buffers".  In contrast, in Emacs 26, the popped up buffer *Ibuffer
confirmation* does not get added to the *Ibuffer* display and thus is
not counted by `ibuffer-map-lines'.

AFAICT, this difference is not due to any ibuffer code changes after
Emacs 26; rather, there appears to be a timing difference with respect
to when Emacs updates the *Ibuffer* display: when I instrument
`ibuffer-update' for Edebug and then type `x' (step 5 above), what
happens in Emacs 26 is that I can confirm with `y', then the flagged
lines are deleted, and only then does Edebug stop the execution so I can
step into `ibuffer-update'; while in Emacs 27+, as soon as I type `x',
Edebug stops execution, i.e., before the flagged lines are deleted.

`ibuffer-update' is called in `ibuffer-auto-update-changed', which is
added to post-command-hook in `ibuffer-auto-mode'.  So it seems that in
Emacs 26 post-command-hook runs or takes effect later than in Emacs 27+.
Whether this is really the case, and if so, what change it is due to, I
haven't determined, and I don't know how restore the Emacs 26 execution
order (or if that's even desirable).  But even if the difference is due
to something else, the message displayed in Emacs 27+ after the deletion
of the *Ibuffer* lines is at least misleading, since it clearly is meant
to refer only to the flagged lines, as in Emacs 26.

In lieu of a real fix, since it is, AFAICS, only the transient buffer
*Ibuffer confirmation* that results in the problematic message, a
workaround is simply to decrement the line count by one when
ibuffer-auto-mode is enabled, as in the the attached patch (which also
takes the opportunity to wrap an overlong line in `ibuffer-map-lines').


In GNU Emacs 30.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version
 3.24.37, cairo version 1.17.6) of 2023-06-22 built on strobelfs
Repository revision: a23a09a82fc59402f1f7c23a46c65fc7001eecdf
Repository branch: master
Windowing system distributor 'The X.Org Foundation', version 11.0.12101008
System Description: Linux From Scratch r11.3-65

Configured using:
 'configure -C --with-xwidgets 'CFLAGS=-Og -g3'
 PKG_CONFIG_PATH=/opt/qt5/lib/pkgconfig'

Configured features:
ACL CAIRO DBUS FREETYPE GIF GLIB GMP GNUTLS GPM GSETTINGS HARFBUZZ JPEG
JSON LCMS2 LIBSYSTEMD LIBXML2 MODULES NOTIFY INOTIFY PDUMPER PNG RSVG
SECCOMP SOUND SQLITE3 THREADS TIFF TOOLKIT_SCROLL_BARS TREE_SITTER WEBP
X11 XDBE XIM XINPUT2 XPM XWIDGETS GTK3 ZLIB